A: miRiadne implements four slightly different “Rosetta” functions and one TimeWarp function. The Rosetta functions are used to translate, update miRNA lists and datsets, and to find the common miRNAs between datasets, platforms or miRBase versions. The TimeWarp function allows to browse and visualize the nomenclature’s evolution across miRBase versions.

Q: What is the format requirement for my input miRna list?

A: lists of miRNA names can be directly typed or copied/pasted in the forms separated by commas or new lines. miRNA lists can be saved as tab delimited or comma separated value files then dragged and dropped inside the forms. Datasets (i.e. matrices of miRNA names and expression values) should be in csv or tab delimited files with matrix format: the first column must contain the miRNA names.

Q: Does miRiadne limit the maximum number of miRNAs in a list?

A: No, but longer lists will take longer to be parsed and processed.

Q: Who can use miRiadne, and at what cost?

A: miRiadne is free to use for all user.

Q: Where does miRiadne knowledgebase come from?

A: miRiadne integrates the entire miRBase databases, from version 10 to the most recent (version 21) and the annotation information files (AIFs) of 25 different miRNA detection platforms from 9 vendors. When AIFs contained information about miRNA mature sequence these were retrieved, otherwise mature sequences were retrieved from the miRBase version that specific platform rely on, as claimed by the vendor.

Q: Can I access all the database files? (platform files)

A: Not with the web based application; if interested please contact us.

Q: How often do you update miRiadne?

A: We strive to update miRiadne every time the miRBase publishes a new release, and - at a irregular base - to add new detection platform that may become available.

Q: Who do I contact if I find an annotation error?

A: Please contact us using following the instructions in the Contacts section of the web site.

Q: How do I cite miRiadne

A: miRiadne is not published yet. As soon it will be published we will prompt to use the publication citation; so far you can acknowledge miRiadne by its own URL.

Q: Not all of my miRNAs are converted! Why?

A: Many could be the reasons why. You should receive a warning if any of your input miRNA name is not converted. The main reasons are: i) an erroneous selection of origin platform; ii) a misannotated - not original or manipulated - dataset file from a miRNA detection platform; iii) a dataset that is obtained merging multiple platforms. You can use the TimeWarp function with relaxed option selected to see if your input is consistent with your selection (either be it a platform or a miRBase version).

Q: What are the system/browser requirements to run miRiadne?

A: miRiadne should be smoothly useable on all major and most recent browsers: Mozilla Firefox, Chrome, Safari, IE.

Q: How many specie have miRNA information deposited in miRiadne?

A: miRiadne contains information from the whole miRBases, thus all specie in miRBase are deposited. Nonetheless, the four Rosetta functions are implemented for human miRNAs only (beginning with the hsa prefix), while the TimeWarp function is already implemented on all specie allowing to search for any miRNA.
We are planning to extend the Rosetta function to rodent miRNAs too (miRNA with “-mmu” and “-rno” prefix).

Q: Are my data kept or saved permanently?

A: No, we are not storing your data. The input is processed and kept just for the time needed for the processing. The download files are temporary and are discarded closing the web page or ending the session.

Q: Are there other tools similar to miRiadne?

A: Yes, but be aware that they are not platform centric. You can use other tools to track miRNA names evolution across miRBase version. These tools are: miRBase Tracker, miRBase, miRConverter

If you find this service useful and/or you are using it for any scientific or commercial purposes please cite us: